I am using Pixel Classification in Ilastik to export for segmentation in Cell Profiler. We recently began taking larger images, and I was working with an image in Ilastik that was about 500 x 9000 pixels. I am working on a laptop in Windows 10 with 64GB RAM. When I tried to export probabilities as a tiff sequence, as we usually do, I received an error that there was not enough RAM to export to the selected format (it only worked when I cropped the image to a lower size). There were no other significant programs running in the background, and only about 10% of memory was being used. However, when I tried to export the exact same file on my personal 2011 Macbook Pro with only 16GB RAM, it was able to export the entire file.

This problem remained in both Ilastik 1.3.2 and 1.3.0 after reinstallation. I was wondering if there is some issue with a Mac vs PC in terms of how RAM is allocated to Ilastik, or if there is any way to allocate more RAM to Ilastik or some other solution to this problem.

I don’t see a file with the name .ilastikrc
To clarify, do I just create a text file with those 2 lines?

Is it possible that, for some reason, Ilastik’s RAM usage is currently limited, and I could increase by writing a larger value? For example, if the computer has 64GB of RAM, could I create that text file and write 64000 for <MEMORY_IN_MB> to actually increase the RAM allocated to Ilastik?

I think I have misread your first post. So you really had only one image with 500 x 9000? That should, in any case not use more that 1 GB of your RAM.

Could you do us a favor and, on your windows machine delete the log file (found at C:\Users\<YourUserName>\ilastik_log.txt), start ilastik again, do the export that results in the error, and send us the log file to team@ilastik.org?

Hey @Zavi, I looked into it some more and could you please give me a bit more information on the image you are using? Is it’s size really just 500x9000? Furthermore, to which data type are you exporting? float, or uint16…? Also are you reshuffeling the axis order to cyx before you export?

In any case we’ve figured out the problem (it is related to default number types that are used by numpy, the numerical library we use, which are different on windows…)
Will be fixed in the next release - thank you very much for discovering/reporting this issue!!

For more information: the size is 511 x 9063. I tried cropping a few sizes to see what would export, and it worked once I got the width lower than about 5500 (i.e. 511 x 5500). For our export, I was using unsigned 8 bit (though I think I had the same issue attempting with unsigned 16 bit), transposing axis order to cyx, and formatting as a tiff sequence.

Glad to hear you figured out the problem, looking forward to the fix in the next release! Any sense of the timing on that release?

this didn’t make it, unfortunately. However, we’re releasing an update of our fiji import/export plugin that is much faster, and hence, you can just export to h5 and convert in fiji, if tiff stacks is what you need.
Will post about this update, here, too.